Systematic review of human gut resistome studies revealed variable definitions and approaches.
Ontology highlight
ABSTRACT:
SUBMITTER: Ho J
PROVIDER: S-EPMC7524153 | biostudies-literature | 2020 Nov
REPOSITORIES: biostudies-literature
Publications
Systematic review of human gut resistome studies revealed variable definitions and approaches.
Ho Jeffery J Yeoh Yun Kit YK Barua Nilakshi N Chen Zigui Z Lui Grace G Wong Sunny H SH Yang Xiao X Chan Martin Cw MC Chan Paul Ks PK Hawkey Peter M PM Ip Margaret M
Gut microbes 20200116 1
In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 months prior to sampling. In studies with <i>de novo</i> assembly, AR genes were identified based on variable nucleotide or amino acid sequence similaritie ...[more]
Similar Datasets
Project description:BackgroundResearchers use different definitions to identify children with asthma in epidemiological surveys. We conducted a systematic review to describe the definitions used in epidemiologic studies for wheeze and asthma in the paediatric population, aimed to inform the development of a uniform definition of paediatric asthma for future epidemiological research.MethodsWe systematically searched terms to identify asthma and/or wheeze among children aged <13 years and published between 1995-2020 across seven databases (MEDLINE, EMBASE, PsycINFO, Global Health, AMED, LILACS and CINAHL). PRISMA guidelines were followed for this review.ResultsWe extracted a total of 11 886 records, where 190 met our eligibility criteria and included in the analysis. Among the included studies, 62.1% (n = 118/190) used the International Study of Asthma and Allergies in Childhood (ISAAC) questionnaires, predominantly in developing countries (80%, n = 64/80). 'Wheeze' was reported in five categories, subdivided by 14 different definitions. "Current wheeze", defined as caregivers report of wheezing sounds from the chest of the child in the past 12 months and "Wheeze ever", defined as caregivers' report of wheezing or whistling in the chest of the child at any previous time, were the most common wheeze category reported in 129 and 95 studies, respectively. Asthma was reported in nine categories using 53 definitions. The most common asthma category was "Asthma ever", which was reported in 89 studies, based on caregiver statement that the child had asthma in the past.ConclusionDefinitions of wheeze and asthma for children used in surveys are primarily based on parent-reported clinical features. Studies from developing countries more frequently used the ISAAC definitions to report childhood asthma and wheeze compared to the studies from developed counties. The use of a uniform asthma definition will aid the interpretation of research findings globally.
| S-EPMC8285759 | biostudies-literature
Project description:Introduction: Hypertension is one of the major risk factors to human health and human studies on association between gut microbiota and hypertension or blood pressure have received increased attention. In the present study, we aim to evaluate gut microbiota dysbiosis in human hypertension using a method of systematic review. Methods: PubMed, EMBASE, and Web of Science databases were searched until March 2021 to identify eligible articles. Additional articles were also identified by searching specific authors in this field. Inclusion criteria were observational studies based on stool samples with hypertension group and control group. Newcastle-Ottawa quality assessment scale (NOS) was used to assess the quality of the included studies. PROSPERO registration number: CRD42020212219. Results: A total of 17 studies enrolling 9,085 participants were included. Fifteen of the enrolled studies showed good quality and two studies showed fair quality based on NOS. We found alpha diversity in hypertension decreased significantly and microbial structure can be separated compared with control groups. Gut microbiota of hypertension showed depletion of short chain fatty acids (SCFAs) producers and over-growth of some Proteobacteria and Bacteroidetes members. Up-regulation of lipopolysaccharide biosynthesis, phosphotransferase system, ABC transporters, etc. and down-regulation of some amino acid metabolism, etc. in hypertension were reported. Fecal SCFAs levels increased and plasma SCFAs levels decreased in hypertension. Stronger microbial interactions in hypertension were seen. Conclusion: In conclusion, gut microbiota dysbiosis was observed in hypertension, including decreased diversity, altered microbial structure, compositional change of taxa, alterations of microbial function, nutritional and immunological factors, and microbial interactions. Poor absorption and high excretion of SCFAs may play an important role in the pathogenesis of hypertension. These findings may provide insights into etiology study and new microbial-based therapies of hypertension. Systematic Review Registration: PROSPERO database, identifier CRD42020212219.
| S-EPMC8160125 | biostudies-literature
Project description:The antibiotic resistance crisis underlies globally increasing failures in treating deadly bacterial infections, largely due to the selection of antibiotic resistance genes (ARG) collection, known as the resistome, in human gut microbiota. So far, little is known about the relationship between gut antibiotic resistome and host metabolic disorders such as type 2 diabetes (T2D). Here, metagenomic landscape of gut antibiotic resistome is profiled in a large multiomics human cohort (n = 1210). There is a significant overall shift in gut antibiotic resistome structure among healthy, prediabetes, and T2D groups. It is found that larger ARG diversity is associated with a higher risk of T2D. The novel diabetes ARG score is positively associated with glycemic traits. Longitudinal validation analysis confirms that the ARG score is associated with T2D progression, characterized by the change of insulin resistance. Collectively, the data describe the profiles of gut antibiotic resistome and support its close relationship with T2D progression.
| S-EPMC9008416 | biostudies-literature
Project description:BackgroundThe resistome, the collection of antibiotic resistance genes (ARGs) in a microbiome, is increasingly recognised as relevant to the development of clinically relevant antibiotic resistance. Many metagenomic studies have reported resistome differences between groups, often in connection with disease and/or antibiotic treatment. However, the consistency of resistome associations with antibiotic- and non-antibiotic-treated diseases has not been established. In this study, we re-analysed human gut microbiome data from 26 case-control studies to assess the link between disease and the resistome.ResultsThe human gut resistome is highly variable between individuals both within and between studies, but may also vary significantly between case and control groups even in the absence of large taxonomic differences. We found that for diseases commonly treated with antibiotics, namely cystic fibrosis and diarrhoea, patient microbiomes had significantly elevated ARG abundances compared to controls. Disease-associated resistome expansion was found even when ARG abundance was high in controls, suggesting ongoing and additive ARG acquisition in disease-associated strains. We also found a trend for increased ARG abundance in cases from some studies on diseases that are not treated with antibiotics, such as colorectal cancer.ConclusionsDiseases commonly treated with antibiotics are associated with expanded gut resistomes, suggesting that historical exposure to antibiotics has exerted considerable selective pressure for ARG acquisition in disease-associated strains. Video Abstract.
| S-EPMC10386251 | biostudies-literature
Project description:Antibiotic resistance (AR) is indisputably a major health threat which has drawn much attention in recent years. In particular, the gut microbiome has been shown to act as a pool of AR genes, potentially available to be transferred to opportunistic pathogens. Herein, we investigated for the first time changes in the human gut resistome during aging, up to extreme longevity, by analyzing shotgun metagenomics data of fecal samples from a geographically defined cohort of 62 urban individuals, stratified into four age groups: young adults, elderly, centenarians, and semisupercentenarians, i.e., individuals aged up to 109 years. According to our findings, some AR genes are similarly represented in all subjects regardless of age, potentially forming part of the core resistome. Interestingly, aging was found to be associated with a higher burden of some AR genes, including especially proteobacterial genes encoding multidrug efflux pumps. Our results warn of possible health implications and pave the way for further investigations aimed at containing AR accumulation, with the ultimate goal of promoting healthy aging. IMPORTANCE Antibiotic resistance is widespread among different ecosystems, and in humans it plays a key role in shaping the composition of the gut microbiota, enhancing the ecological fitness of certain bacterial populations when exposed to antibiotics. A considerable component of the definition of healthy aging and longevity is associated with the structure of the gut microbiota, and, in this regard, the presence of antibiotic-resistant bacteria is critical to many pathologies that come about with aging. However, the structure of the resistome has not yet been sufficiently elucidated. Here, we show distinct antibiotic resistance assets and specific microbial consortia characterizing the human gut resistome through aging.
| S-EPMC8550338 | biostudies-literature
Project description:Recent evidence has shown a number of extra-skeletal functions of Vitamin D (VD), primarily involving the immune system. One of these functions is mediated by the modulation of gut microbiota, whose alterations are linked to many diseases. Our purpose is to contribute to the understanding of existing evidence on the association between VD and gastrointestinal microbiota alterations. A systematic review of studies with human subjects has been conducted up to January 2021. We included publications reporting the association between gut microbiota and VD, including VD supplementation, dietary VD intake and/or level of 25(OH)D. We identified 25 studies: 14 were interventional and 11, observational. VD supplementation was found to be associated with a significant change in microbiome composition, in particular of Firmicutes, Actinobacteria and Bacteroidetes phyla. Furthermore, Firmicutes were found to be correlated with serum VD. Concerning alpha and beta diversity, a high nutritional intake of VD seems to induce a shift in bacterial composition and/or affects the species' richness. Veillonellaceae and Oscillospiraceae families, in the Firmicutes phylum, more frequently decreased with both increasing levels of 25(OH)D and vitamin D supplementation. We found evidence of an association, even though the studies are substantially heterogeneous and have some limitations, resulting sometimes in conflicting results. To further understand the role of VD on the modulation of the gastrointestinal microbiota, future research should be geared toward well-designed animal-based studies or larger randomized controlled trials (RCTs).
| S-EPMC8540279 | biostudies-literature
Project description:BackgroundIntermittent fasting (IF) has gained popularity in interventions targeting overweight, obesity and metabolic syndrome. IF may affect the gut microbiome composition and therefore have various effects on gut microbiome mediated functions in humans. Research on the effects of IF on human gut microbiome is limited. Therefore, the objective of this systematic review was to determine how different types of IF affect the human gut microbiome.MethodsA literature search was conducted for studies investigating the association of different types of IF and gut microbiota richness, alpha and beta diversity, and composition in human subjects. Databases included Cochrane Library (RRID:SCR_013000), PubMed (RRID:SCR_004846), Scopus (RRID:SCR_022559) and Web of Science (RRID:SCR_022706). A total of 1,332 studies were retrieved, of which 940 remained after removing duplicates. Ultimately, a total of 8 studies were included in the review. The included studies were randomized controlled trials, quasi-experimental studies and pilot studies implementing an IF intervention (time-restricted eating, alternate day fasting or 5:2 diet) in healthy subjects or subjects with any disease.ResultsMost studies found an association between IF and gut microbiota richness, diversity and compositional changes. There was heterogeneity in the results, and bacteria which were found to be statistically significantly affected by IF varied widely depending on the study.ConclusionThe findings in this systematic review suggest that IF influences gut microbiota. It seems possible that IF can improve richness and alpha diversity. Due to the substantial heterogeneity of the results, more research is required to validate these findings and clarify whether the compositional changes might be beneficial to human health.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/, identifier CRD42021241619.
| S-EPMC10894978 | biostudies-literature
Project description:T cells recognize their ligand, the peptide major histocompatibility complex (MHC), via the T-cell receptor (TCR), which is composed of covalently linked α and β or γ and δ chains. This recognition is critical for T-cell ontogeny and controls the selection, activation, and function of T lymphocytes. Specific TCR αβ variable regions have been associated with immunopathogenesis of Chagas disease. Here, we present a systematic review that compiles experimental in vivo and human data regarding the preferential expression of variable alpha (Vα) and variable beta (Vβ) chain regions in Trypanosoma cruzi infection. The original studies indexed in PubMed/Medline, Scopus, and Web of Science databases were screened according to the PRISMA strategy. The analysis showed that expression of TCR Vα subfamilies were evaluated in one human study, and, unlike TCR Vβ, TCR Vα presented a more restricted usage. Despite the great variability in the usage of TCR Vβ regions in human Chagas disease, a down-regulation of TCR Vβ5 expression by T cells from patients in the acute phase of the disease was shown. Opposingly, this TCR region was found overly expressed in CD4+ T cells from chronic Chagas patients. It was also demonstrated that murine Vβ9+ T cells derived from nonlymphoid organs of T. cruzi-infected animals had a modulatory profile, while splenic Vβ9+ T cells produced inflammatory cytokines, indicating that although they display the same TCR Vβ region usage, these cells are functionally distinct. Despite the limitations of few papers and year of publication of the studies, compiling the data derived from them reveals that further investigation of TCR usage will point to their potential role in protective or pathogenic responses, as biomarkers of disease progression, and in the search for dominant peptides potentially useful for the development of vaccines or therapies. Author summary Chagas disease is a neglected tropical disease, caused by infection with Trypanosoma cruzi. Differential expression of certain T-cell receptor (TCR) variable regions has been associated with the immunopathogenesis of Chagas disease. Here, we present a systematic review that compiled experimental in vivo and human data regarding the preferential expression of TCR alpha and beta chain variable regions in Chagas disease. The original studies indexed in the PubMed/Medline, Scopus, and Web of Science databases were screened according to the PRISMA strategy. Despite the great variability in the use of TCR Vβ in T. cruzi infection, the outcomes indicate that there is a down-regulation of TCR Vβ5 expression in T cells from patients in the acute phase of Chagas disease. However, this region is preferentially expressed by CD4+ T cells from chronic Chagas patients. Additionally, it has been demonstrated that murine Vβ9+ T cells derived from nonlymphoid organs displayed a modulatory profile, while splenic Vβ9+ T cells produced inflammatory cytokines, indicating that although they express the same TCR Vβ region, these cells are functionally distinct. Information on TCR expression, specificity and function have critical impact on vaccine design.
| S-EPMC9477334 | biostudies-literature
Project description:AbstractWe created ResistoMap—a Web-based interactive visualization of the presence of genetic determinants conferring resistance to antibiotics, biocides and heavy metals in human gut microbiota. ResistoMap displays the data on more than 1500 published gut metagenomes of world populations including both healthy subjects and patients. Multiparameter display filters allow visual assessment of the associations between the meta-data and proportions of resistome. The geographic map navigation layer allows to state hypotheses regarding the global trends of antibiotic resistance and correlates the gut resistome variations with the national clinical guidelines on antibiotics application.Availability and implementationResistoMap was implemented using AngularJS, CoffeeScript, D3.js and TopoJSON. The tool is publicly available at http://resistomap.rcpcm.org.Contactyarygin@phystech.edu.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC5870722 | biostudies-literature
Project description:BackgroundQuality of reporting for Randomized Clinical Trials (RCTs) in oncology was analyzed in several systematic reviews, but, in this setting, there is paucity of data for the outcomes definitions and consistency of reporting for statistical tests in RCTs and Observational Studies (OBS). The objective of this review was to describe those two reporting aspects, for OBS and RCTs in oncology.MethodsFrom a list of 19 medical journals, three were retained for analysis, after a random selection: British Medical Journal (BMJ), Annals of Oncology (AoO) and British Journal of Cancer (BJC). All original articles published between March 2009 and March 2014 were screened. Only studies whose main outcome was accompanied by a corresponding statistical test were included in the analysis. Studies based on censored data were excluded. Primary outcome was to assess quality of reporting for description of primary outcome measure in RCTs and of variables of interest in OBS. A logistic regression was performed to identify covariates of studies potentially associated with concordance of tests between Methods and Results parts.Results826 studies were included in the review, and 698 were OBS. Variables were described in Methods section for all OBS studies and primary endpoint was clearly detailed in Methods section for 109 RCTs (85.2%). 295 OBS (42.2%) and 43 RCTs (33.6%) had perfect agreement for reported statistical test between Methods and Results parts. In multivariable analysis, variable "number of included patients in study" was associated with test consistency: aOR (adjusted Odds Ratio) for third group compared to first group was equal to: aOR Grp3 = 0.52 [0.31-0.89] (P value = 0.009).ConclusionVariables in OBS and primary endpoint in RCTs are reported and described with a high frequency. However, statistical tests consistency between methods and Results sections of OBS is not always noted. Therefore, we encourage authors and peer reviewers to verify consistency of statistical tests in oncology studies.
| S-EPMC5055310 | biostudies-literature